library(Hmisc) # library for 'rcorr()' function

TOMCAT <- read.table("cohesionMetricsFinal_Tomcat_tab.txt", header=TRUE, sep="\t"); # readinng the data
rcorr(as.matrix(TOMCAT), type="spearman") # running correlation (it considers pairwise deletion for missing values)

RHINO <- read.table("cohesionMetricsFinal_Rhino_tab.txt", header=TRUE, sep="\t")
rcorr(as.matrix(RHINO), type="spearman")

JFREECHART <- read.table("cohesionMetricsFinal_JFreeChart_tab.txt", header=TRUE, sep="\t")
rcorr(as.matrix(JFREECHART), type="spearman")

JEDIT <- read.table("cohesionMetricsFinal_jEdit_tab.txt", header=TRUE, sep="\t")
rcorr(as.matrix(JEDIT), type="spearman")

FINDBUGS <- read.table("cohesionMetricsFinal_Findbugs_tab.txt", header=TRUE, sep="\t")
rcorr(as.matrix(FINDBUGS), type="spearman")

FREECOL <- read.table("cohesionMetricsFinal_Freecol_tab.txt", header=TRUE, sep="\t")rcorr(as.matrix(JEDIT), type="spearman")
rcorr(as.matrix(FREECOL), type="spearman")